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# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Module for interfacing with phonopy, see https://atztogo.github.io/phonopy/
"""
from typing import Dict, List, Any
import numpy as np
from monty.dev import requires
from monty.serialization import loadfn
from scipy.interp... | vorwerkc/pymatgen | pymatgen/io/phonopy.py | Python | mit | 25,292 | [
"phonopy",
"pymatgen"
] | 189cce12a4724d9ba9083a272cb97726d2eaa8f3abe26f7c43c6bca9aefae542 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio-Client.
# Copyright (C) 2014 CERN.
#
# Invenio-Client is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at your opt... | SamiHiltunen/invenio-client | invenio_client/connector.py | Python | gpl-2.0 | 18,049 | [
"VisIt"
] | 1258b93d0a77f154eab276fd132dd023f1232e6b9d6344f03d3d9a473a3cc215 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | govarguz/espressopp | src/interaction/AngularHarmonic.py | Python | gpl-3.0 | 5,154 | [
"ESPResSo"
] | a15c68f9a3c0ed3a619609d5eae6a54d3cd4577420c98c1dd02ae6f003c8c6f9 |
#!/usr/bin/env python
"""
Copyright 2001 Pearu Peterson all rights reserved,
Pearu Peterson <pearu@ioc.ee>
Permission to use, modify, and distribute this software is given under the
terms of the LGPL. See http://www.fsf.org
NO WARRANTY IS EXPRESSED OR IMPLIED. USE AT YOUR OWN RISK.
$Revision: 1.1 $
$Date:... | chunshen1987/iSS | utilities/for_paraview/lib152/Scalars.py | Python | mit | 1,178 | [
"VTK"
] | f1cf92e10982d1a7919e2e1c88f6eff08f488da0b9225fa5ff087841538e5470 |
#!/usr/bin/env python
# This is the script that runs a testing python script.
# The script to be run must be the first argument.
import sys
if len(sys.argv) < 2:
print "Usage %s <test script> [<addition arguments>]" % sys.argv[0]
sys.exit(1)
for i in range(2, len(sys.argv)):
if sys.argv[i] == '-A' and i < l... | naucoin/VTKSlicerWidgets | Utilities/vtkTclTest2Py/rtImageTest.py | Python | bsd-3-clause | 3,453 | [
"VTK"
] | 2be6a5bfc9e80c5aca6a51afe066a8ac758813210b27c09b3f5f2a7c66ae5a02 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | natanielruiz/android-yolo | jni-build/jni/include/tensorflow/python/ops/gradients.py | Python | apache-2.0 | 29,579 | [
"VisIt"
] | 3a9b3cc989c5c3ddb8ec5bd030bd636dd28a68cab3397fcc3ee71d76d2963d24 |
import sys
sys.path.append('..')
import pytest
import os.path
import unittest
from nyctext import nycaddress as parser
class Address(unittest.TestCase):
def __init__(self, *args, **kwds):
super(Address, self).__init__(*args, **kwds)
self.cwd = os.path.dirname(__file__)
def checkExpectation(... | cds-amal/addressparser | tests/testAddresses.py | Python | mit | 7,092 | [
"COLUMBUS"
] | 2548d5f72017c7121b9bb49c39e389e47f047951ba655f325a9a57adbb170aee |
"""
===========
Description
===========
bbcflib is a set of Python modules for accessing facilities used by
the Bioinformatics and Biostatistics Core Facility (BBCF) at the EPFL.
It provides modules for BBCF's
* *GenRep* (genome data repository),
* the LIMS of the DNA Array Facilities at UNIL and UNIGE,
* the standar... | bbcf/bbcflib | bbcflib/__init__.py | Python | gpl-3.0 | 1,826 | [
"pysam"
] | e45a76589d8ece75ce5e6da1b17c260744b96cfcbbdd8f3d0cb05b4364124d42 |
import math
import random
import copy
import pickle
"""
multilayer neural network.
This version is designed for effeciency so is less object oriented.
The bias input in implemented by adding an extra weight to each set of inputs.
The weights are stored as an 3 dimensional array [layers][neurons_in_layer][weight... | pauljohnleonard/pod-world | CI_2014/ATTIC/OLD_SIMULATION_CODE/CartWithIP/brain.py | Python | gpl-2.0 | 7,638 | [
"NEURON"
] | 711480f6597589ea36b29853a20de7cc10ad17a2d25e932fcdce81a8b70b30fa |
#!/usr/bin/python
"""
Copyright 2013 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of th... | clreinki/GalaxyHarvester | ghObjects.py | Python | agpl-3.0 | 29,278 | [
"Galaxy"
] | 6f44a5ea1c97b2a696371056b28d42793093598b1d74c82356f113de155bad51 |
# -----------------------------------------------------------------------------
# Download data:
# - Browser:
# http://midas3.kitware.com/midas/folder/10409 => VisibleMale/vm_head_frozenct.mha
# - Terminal
# curl "http://midas3.kitware.com/midas/download?folders=&items=235235" -o vm_head_frozenct.mha
# ----... | Kitware/tonic-data-generator | scripts/vtk/medical/head-ct.py | Python | bsd-3-clause | 3,738 | [
"VTK"
] | 5f96f3812ffff6c9d0422535ec70c68e17583ffa998c7423e9dbef7a67387363 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides objects to inspect the status of the Abinit tasks at run-time.
by extracting information from the main output file (text format).
"""
from __future__ import unicode_literals, division, p... | xhqu1981/pymatgen | pymatgen/io/abinit/abiinspect.py | Python | mit | 19,214 | [
"ABINIT",
"CRYSTAL",
"pymatgen"
] | e92033f92cdd095bf33672189bd904de44bf6b02d576738aff9c146ee582077c |
#!/usr/bin/env python
# The glassbrain class copied from The NeuroImaging Analysis Framework (NAF) repositories
# The code is covered under GNU GPL v2.
# Usage example.
'''
brain = ConnecBrain("fsaverage", "lh", "inflated")
coords = np.array([[-27., 23., 48.],
[-41.,-60., 29.],
[-64., -20., -9.],
... | fboers/jumegX | glassbrain.py | Python | bsd-3-clause | 8,410 | [
"Mayavi"
] | 409824126e482a66e2a99e041c1a6e0582a7ec7de9b7080dd9a500cd3c0dd87e |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Feb 23 16:02:10 2018
@author: BallBlueMeercat
"""
import matplotlib.pyplot as plt
from emcee import EnsembleSampler
import numpy as np
import time
import os.path
import datasim
import tools
import ln
import plots
def stats(params, zpicks, mag, sigma, ... | lefthandedroo/Cosmo-models | zprev versions/Models_py_backup/stats.py | Python | mit | 6,851 | [
"Gaussian"
] | b23e310e64dfd1a814f08ac236143878f95251b7765f2f7d2d32d0819aa8243c |
""" Munch is a subclass of dict with attribute-style access.
>>> b = Munch()
>>> b.hello = 'world'
>>> b.hello
'world'
>>> b['hello'] += "!"
>>> b.hello
'world!'
>>> b.foo = Munch(lol=True)
>>> b.foo.lol
True
>>> b.foo is b['foo']
True
It is safe to import * from th... | pombredanne/bunch | munch/__init__.py | Python | mit | 14,119 | [
"Brian"
] | 266bd0eec3d86b55e7b3201c9a2a421d70ba120c5449703793090480ec2f6492 |
""" Refresh local CS (if needed)
Used each time you call gConfig. It keep your configuration up-to-date with the configuration server
"""
import threading
import time
import os
import _thread
from DIRAC.ConfigurationSystem.Client.ConfigurationData import gConfigurationData
from DIRAC.ConfigurationSystem.private.Refre... | DIRACGrid/DIRAC | src/DIRAC/ConfigurationSystem/private/Refresher.py | Python | gpl-3.0 | 3,919 | [
"DIRAC"
] | 360cb88d0b67c45a5b85ff7053a946c34b1f2c6f845dc7e7d42355351e8e291e |
# -*- coding: utf-8 -*-
__author__ = 'shreejoy'
import unittest
import neuroelectro.models as m
from db_functions.normalize_ephys_data import check_data_val_range, normalize_nedm_val
class DataRangeTest(unittest.TestCase):
def test_check_data_val_range_in(self):
ephys_prop = m.EphysProp.objects.create(... | neuroelectro/neuroelectro_org | tests/test_normalize_ephys_data.py | Python | gpl-2.0 | 3,931 | [
"NEURON"
] | 732ebd6a203f97beb5e57c0b434f6e08d36ab9e9f712648b48cc146acb6854f0 |
# Part of Neubot <https://neubot.nexacenter.org/>.
# Neubot is free software. See AUTHORS and LICENSE for more
# information on the copying conditions.
''' Path management utils '''
import collections
import logging
import os
from .third_party import six
from .third_party.six.moves.urllib import parse as urlparse
... | neubot/neubot-runtime | neubot_runtime/utils_path.py | Python | gpl-3.0 | 4,653 | [
"VisIt"
] | 3b2e269e573eeb20aa3dc3d30a423b6c6ec675ddb5cae3bec1a80181ae218b7f |
# thic code is used to test Python2Vtk.py read and write function
import tempfile as TP
import numpy as np
from MNNparcellation import Python2Vtk as PY
def co_shape(A, B):
if np.shape(A) == np.shape(B):
return A, B, 1
elif np.shape(A) == np.shape(B.T):
return A, B.T, 1
else:
retu... | BBELAOUCHA/dMRIParcellation | test/test_vtk_readwrite.py | Python | bsd-3-clause | 1,591 | [
"VTK"
] | ad7758ea72f2191bb970098931b3ab550ca7349004f1d568e1830c25e0f64733 |
import json
import pkg_resources
import re
import string
import time
from pymongo import MongoClient
import misc
import parser_helpers
import utils
# Initialize global variables
phone_num_sets = misc.phone_num_lists()
countries = utils.countries()
post_id_bp_groups = utils.post_id_backpage_groups()
# read ethnicit... | usc-isi-i2/etk | etk/data_extractors/htiExtractors/parser.py | Python | mit | 27,555 | [
"CRYSTAL"
] | c115db4b515cba4c4bc029dd8310eb68a2f3ce6ab42749250bf44f3addbe58bb |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# gauss2d.py
"""
Class for generating and fitting 2D Gaussian peaks
Supports both least squares and MLE fitting and gaussian peaks
parameterized by a single width, widths along each axis and widths
along arbitrary axes. Fitting can be done with manually specified
guesses o... | david-hoffman/peaks | peaks/gauss2d.py | Python | apache-2.0 | 36,593 | [
"Gaussian"
] | 14685466c4c67affe5b943dda4b6f75b7c0c7996728a5b1bd1caf2a4ae769a9e |
# ----------------------------------------
# USAGE:
# python water_positioning.py config_file
# ----------------------------------------
# PREAMBLE:
import numpy as np
import sys
import os
import MDAnalysis
from MDAnalysis.analysis.align import *
from distance_functions import *
flush = sys.stdout.flush
zeros = np... | rbdavid/DENV-NS3h | Water_positioning/water_positioning.py | Python | gpl-3.0 | 4,826 | [
"MDAnalysis"
] | e6695d5f6bafcf5bf295d8c037d2913414e5123bb4eab834dc74137def1f0b36 |
""" VirtualMachineDB Integration Tests
"""
import unittest
import DIRAC
DIRAC.initialize() # Initialize configuration
from DIRAC.WorkloadManagementSystem.DB.VirtualMachineDB import VirtualMachineDB
class VirtualMachineDBInstanceTests(unittest.TestCase):
"""This tests the instance related database functions.
... | DIRACGrid/DIRAC | tests/Integration/WorkloadManagementSystem/Test_VirtualMachineDB.py | Python | gpl-3.0 | 10,957 | [
"DIRAC"
] | 2eddbd96805c2cdc9e7559eecd96822ba96649fe9d4ce67d53079fd51712d719 |
import vtk, ctk, slicer
import logging
import time
import gc
from slicer.util import VTKObservationMixin
from slicer.ScriptedLoadableModule import *
class LogicMixin(ScriptedLoadableModuleLogic, VTKObservationMixin):
def __init__(self, ModuleNodeName):
VTKObservationMixin.__init__(self)
self.InputCases = ... | NIRALUser/SPHARM-PDM | Modules/Scripted/ShapeAnalysisModule/CommonUtilities/LogicMixin.py | Python | apache-2.0 | 3,223 | [
"VTK"
] | 4ac7730d55e026c8ee3ca11bf117226e07e9f102eabad8e1495a6b15298a140d |
"""
Unit tests for ASP solving.
"""
import unittest
from collections import defaultdict
from neural_world.tests import NeuralNetworkTester
class TestASPSolving(NeuralNetworkTester):
def test_no_atoms(self):
atoms = ''
expected_result = ''
self.assert_running(atoms, expected_result)
... | Aluriak/neural_world | neural_world/tests/test_asp_solving.py | Python | gpl-2.0 | 3,626 | [
"NEURON"
] | 610a73f426bfd8500be7d57cb8503484e1e30e8b3dbd44792e699115e2fc1769 |
"""
Artificial Intelligence for Humans
Volume 1: Fundamental Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2013 by Jeff Heaton
Licensed under the Apache License, Version 2.0 (the "License");
... | trenton3983/Artificial_Intelligence_for_Humans | vol1/python-examples/lib/aifh/train.py | Python | apache-2.0 | 13,693 | [
"VisIt"
] | b184dd812ea017ab1b5cd046d8468e04bb0b4c4db0069068385bacf4426b89c9 |
from django.db import models
class Locator(models.Model):
subject_identifier = models.CharField(
verbose_name="Subject Identifier",
null=True, blank=True,
max_length=100)
subject_cell = models.CharField(
verbose_name='Cell number',
max_length=100,
blank=True,
... | botswana-harvard/edc-sms | edc_sms/tests/models.py | Python | gpl-2.0 | 1,708 | [
"VisIt"
] | f07067b7971afe4fe85c63db781d9b7e617edaf4c5f9afa5e364c28ecee7c231 |
#!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from parlai.core.build_data import DownloadableFile
import parlai.core.build_data as build_data
import os
RESOURCES = [... | facebookresearch/ParlAI | parlai/tasks/casino/build.py | Python | mit | 1,722 | [
"CASINO"
] | afdd28fb03185bd04cf1c888eddb720e1488638baff3dc253633ba4a45473e00 |
"""User-friendly public interface to polynomial functions. """
from __future__ import print_function, division
from sympy.core import (
S, Basic, Expr, I, Integer, Add, Mul, Dummy, Tuple
)
from sympy.core.mul import _keep_coeff
from sympy.core.symbol import Symbol
from sympy.core.basic import preorder_traversal
... | antepsis/anteplahmacun | sympy/polys/polytools.py | Python | bsd-3-clause | 174,979 | [
"Gaussian"
] | 847d20c8e0b8801413e2a17fb6244f1289f2fdd98be65dd384f48fd38ca39503 |
#!/usr/bin/env python
# Copyright 2015 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
import idl_schema
import json_parse
from js_externs_generator import JsExternsGenerator
from datetime import datetime
import model
impo... | ltilve/ChromiumGStreamerBackend | tools/json_schema_compiler/js_externs_generator_test.py | Python | bsd-3-clause | 8,190 | [
"exciting"
] | cb52cf2478e902799c26b31a7b98115d543c4994482deda09af59d1b1ee3c92e |
# This example demonstrates a multiscale model with synaptic input, Ca
# entry to the spine, receptor modulation following phosphorylation and
# Ca diffusion from spine to the dendrite. Lots going on.
# System switches to a potentiated state after a 1s strong synaptic input.
#
# Ca+CaM <===> Ca_CaM; Ca_CaM + CaM... | dilawar/moose-core | devel/fixme/test_82_multiscale_gluR_phosph_3compt.py | Python | gpl-3.0 | 5,024 | [
"MOOSE"
] | a213e5e3f4357a5b71fc6b0bc698c21c18e3fda3e62baf8dbae289a1fa705de5 |
# -*- coding: utf-8 -*-
import os, codecs
import copy
from structs import Tincture, Fieldless, Charge
TINCTURES = {
'(fieldless)': Fieldless(),
'(tinctureless)': Fieldless(),
'multicolor': Tincture('multicolor'),
}
TINCTURE_ALIASES = {
'azure': ['de larmes'],
'sable': ['de poix'],
'purpure': ... | xavidotron/blazon | words.py | Python | mit | 19,553 | [
"FLEUR"
] | 0845d154c7459f73eabd98b020a77e2124ad82fcb95cd0c04481fed841943247 |
r"""
This module is a VTK Web server application.
The following command line illustrate how to use it::
$ vtkpython .../vtk_web_filebrowser.py --data-dir /.../server_directory_to_share
Any VTK Web executable script come with a set of standard arguments that
can be overriden if need be::... | hlzz/dotfiles | graphics/VTK-7.0.0/Web/Applications/FileBrowser/server/vtk_web_filebrowser.py | Python | bsd-3-clause | 2,963 | [
"VTK"
] | ff2033c1f18598e27991d4de429c14ccc80b57a08f9bcf5e5bee114c4a29c29b |
'''
This module performs a few early syntax check on the input AST.
It checks the conformance of the input code to Pythran specific
constraints.
'''
from pythran.tables import MODULES
from pythran.intrinsic import Class
import ast
class PythranSyntaxError(SyntaxError):
def __init__(self, msg, node=None):
... | artas360/pythran | pythran/syntax.py | Python | bsd-3-clause | 7,358 | [
"VisIt"
] | 9ba82675685767024809a65fa87cd9ca8b2430d43ef38ede232f02a9e986f1cf |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright: (c) 2017, F5 Networks Inc.
# GNU General Public License v3.0 (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
... | brandond/ansible | lib/ansible/modules/network/f5/_bigip_asm_policy.py | Python | gpl-3.0 | 38,806 | [
"Galaxy"
] | 224dc877708cdea9903ae0638b57be819dca67aeb49c46a4c86218fac643c6df |
"""
@name: Modules/House/Lighting/Buttons/__init__.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2020-2020 by D. Brian Kimmel
@license: MIT License
@note: Created on Feb 5, 2020
"""
__updated__ = '2020-02-09'
__version_info__ = (20, 2, 9)
__version__ = '.'.join(map(st... | DBrianKimmel/PyHouse | Project/src/Modules/House/Lighting/Buttons/__init__.py | Python | mit | 727 | [
"Brian"
] | 328a44b94fc92df383f6a545a328f39370eb7fd366a2cc25c82faa0c2177c7ba |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/chronos/src/bigdl/chronos/forecaster/tcmf_forecaster.py | Python | apache-2.0 | 14,725 | [
"ORCA"
] | 15ea11b84fad06ef87037087ed815b669d364a6141fc2b994e0545f80217068e |
""" Decorators for DIRAC.
"""
from __future__ import print_function
import os
import inspect
import functools
import traceback
__RCSID__ = "$Id$"
def deprecated(reason, onlyOnce=False):
""" A decorator to mark a class or function as deprecated.
This will cause a warnings to be generated in the usual log if... | fstagni/DIRAC | Core/Utilities/Decorators.py | Python | gpl-3.0 | 6,569 | [
"DIRAC"
] | a8fac8b05fd839568a33ff64fb5a668adc907001adbb26fc82d81e7167580d03 |
from ase import *
from ase.parallel import paropen
from gpaw import *
from gpaw.wavefunctions.pw import PW
from gpaw.xc.rpa import RPACorrelation
from gpaw.xc.fxc import FXCCorrelation
# LDA --------------------------------------
H = Atoms('H', [(0, 0, 0)])
H.set_pbc(True)
H.center(vacuum=2.0)
calc = GPAW(mode=PW(300... | robwarm/gpaw-symm | doc/tutorials/fxc_correlation/hydrogen.py | Python | gpl-3.0 | 1,311 | [
"ASE",
"GPAW"
] | 689664682b6911316a979e90f48ba7e7f0e22b6328d4f34e5d4c3dc18fc8b3c1 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | var/spack/repos/builtin/packages/perl-moose/package.py | Python | lgpl-2.1 | 2,263 | [
"MOOSE"
] | 1f7dd52e3294a0e341280695c476bdb46c0ab1865b33e80f237f4fc471517544 |
#!usr/bin/python
import matplotlib.pyplot as plt
import matplotlib.widgets as widgets
from mpl_toolkits.mplot3d import Axes3D
import numpy as np
import e_field_gen as e_field
import odeint_solve as ode
import sys as sys
ELEC_MASS = 9.10938356E-31
ELEC_CHARGE = -1.60217662E-19
FUND_FREQ = 3.7474057E14
SP_LI... | KavuriG/classical-calc-three-color | no_gui_tester.py | Python | gpl-3.0 | 4,304 | [
"Gaussian"
] | 2b67ebfeff23823887deb55ebd45ae22e536b0ec9204d45367d44ed7a552fb3c |
#!/usr/bin/env python
#code is same as ~/tools/stats/wiggle_to_simple.py
"""
Read a wiggle track and print out a series of lines containing
"chrom position score". Ignores track lines, handles bed, variableStep
and fixedStep wiggle lines.
"""
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.requi... | volpino/Yeps-EURAC | lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py | Python | mit | 1,292 | [
"Galaxy"
] | 5ba7146e128040a38eb259a2ad167a1f1eb17239fdff7f78d8e9486f69de62c1 |
"""
This is a typical input script that runs a simulation of
laser-wakefield acceleration using Warp 2D / Circ.
Usage
-----
- Modify the parameters below to suit your needs
- Type "python -i warp_script.py" in a terminal
- When the simulation finishes, the python session will *not* quit.
Therefore the simulation c... | openPMD/openPMD-example-datasets | scripts/warp_2d_script.py | Python | cc0-1.0 | 12,337 | [
"Gaussian"
] | dc3fc01676ca7b906513f17b11d64cba62de0ab3d42f399f83819d2dc7b5cbf4 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | sam-m888/gramps | gramps/plugins/webreport/surname.py | Python | gpl-2.0 | 12,157 | [
"Brian"
] | 806704dc9a0e38540b05c05a708897f93d6524b436571023b6e95495b10595ab |
#
# Copyright 2014 James Kermode (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Founda... | libAtoms/matscipy | examples/fracture_mechanics/make_crack_thin_strip/params.py | Python | lgpl-2.1 | 3,464 | [
"ASE",
"Matscipy",
"NetCDF"
] | c6ee7b6aa285fbb31f0624f4c77e712f248e14e0685e92f60a8405d07ec0cb35 |
# French / Français - Translations - Python 3 Only!
from seleniumbase import BaseCase
from seleniumbase import MasterQA
class CasDeBase(BaseCase):
def __init__(self, *args, **kwargs):
super(CasDeBase, self).__init__(*args, **kwargs)
self._language = "French"
def ouvrir(self, *args, **kwargs)... | mdmintz/SeleniumBase | seleniumbase/translate/french.py | Python | mit | 21,271 | [
"VisIt"
] | 3bcbd3d2ed279b64bdc9fb1d05986809cd3807f41a6be55354b2cf09afaf9ab8 |
# Copyright (c) 2021 Ultimaker B.V.
# Cura is released under the terms of the LGPLv3 or higher.
import os
from typing import Dict, List, Optional, Set
from PyQt5.QtNetwork import QNetworkReply
from PyQt5.QtWidgets import QMessageBox
from UM import i18nCatalog
from UM.Logger import Logger # To log errors talking to ... | Ultimaker/Cura | plugins/UM3NetworkPrinting/src/Cloud/CloudOutputDeviceManager.py | Python | lgpl-3.0 | 27,748 | [
"VisIt"
] | 6f3c92ca4f37237d25090824768ff805501e2dd89c15b6d01f2013a27cceddce |
# Copyright 2012 Nebula, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agree... | ankur-gupta91/horizon-net-ip | horizon/base.py | Python | apache-2.0 | 39,012 | [
"VisIt"
] | 18ef71d627e1718809a18e5130b53f0f8508163881ee04677b332e9a6a3313c2 |
#! /usr/bin/env python
# Copyright Ivan Sovic, 2015. www.sovic.org
#
# Creates a pileup from a given SAM/BAM file, and calls consensus bases (or variants).
import os;
import sys;
import operator;
import subprocess;
def increase_in_dict(dict_counter, value):
try:
dict_counter[value] += 1;
except:
dict_counter[v... | isovic/samscripts | src/consensus.py | Python | mit | 26,304 | [
"BWA"
] | eb917c71a4197b7df4b46abefdc13051081a72924504e0cf31c1518337a70048 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Apr 7 19:12:47 2017
@author: roger
"""
# hyperparameter variance: 0.015
import sys
sys.path.append("/Users/roger/Dropbox/TVpgGLM-v1/TVpgGLM")
sys.path.append("/Users/roger/Dropbox/TVpgGLM-v1/TVpgGLM/libs")
import numpy as np
np.random.seed(100)
im... | sheqi/TVpgGLM | runtime/syn_tv_demo1.py | Python | mit | 2,813 | [
"NEURON"
] | aa4355f6c275421a3637e43d4962a32b2d85877edafdc61966f9e1626ee6a04e |
import os
import sys
from gpaw.test import equal
from ase import Atom
from gpaw import GPAW, MixerDif
from gpaw.cluster import Cluster
h = .25
q = 0
box = 3.
spin=True
# B should not have spin contamination
s = Cluster([Atom('B')])
s.minimal_box(box, h=h)
s.set_initial_magnetic_moments([-1])
c = GPAW(xc='LDA', nba... | ajylee/gpaw-rtxs | gpaw/test/spin_contamination.py | Python | gpl-3.0 | 1,116 | [
"ASE",
"GPAW"
] | d76a00896efb002e2607b9e5cd8b2effea8509f1bc252791ed041576d30abdad |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/web/powerstate.py | Python | gpl-2.0 | 5,095 | [
"VisIt"
] | 29f972396c38d9a560692d82ad5974e14a49cb8b8b04075b78c9aba973413de7 |
import numpy as np
import pylab as pl
#--------------------------------------------------------------------
def lens_equation_sie(x1,x2,lpar):
xc1 = lpar[0] #x coordinate of the center of the lens (in units of Einstein radius).
xc2 = lpar[1] #y coordinate of the center of the lens (in units of Einstein... | cavestruz/StrongCNN | image_processing/feature_extraction_methods/mesh_transfer/mesh_trans.py | Python | mit | 8,777 | [
"Galaxy",
"Gaussian"
] | 20665bd447da07fad830b86276de050d5598457e067b049a9a3bf0e5d7a49c91 |
#!/usr/bin/env python
"""
--------------------------------------------------------------------------------
(c) 2017 Julian Rees
License: GNU GPLv3
Description: Plot the performance of the SCF convergence in ORCA.
Run: python scfconvergence.py filename [scfnum skip]
Arguments: filename - file name with extension;
... | julianrees/scripts | python/scfconvergence.py | Python | gpl-3.0 | 3,926 | [
"ORCA"
] | 04265faf3b14af635ce2380da00ed4e3cbf71ef0b72e1b03d9e3793697ba40fe |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
########################################################################
# $HeadURL$
# File : dirac-distribution
# Author : Adria Casajus
########################################################################
"""
Create tarballs for a given DIRAC release
"""
__RCSID... | miloszz/DIRAC | Core/scripts/dirac-distribution.py | Python | gpl-3.0 | 15,635 | [
"DIRAC"
] | 5f1348077a7b4b753d386ef82011ff0aa8f9b16f42f6393bd92a77a18208562e |
#-*- coding: utf-8 -*-
import re, string
import fileinput, codecs, sys
#Reconocimiento de referencias.
apeNomFecTitR = re.compile(ur'(?P<ape>[^,]+), (?P<nom>[^(]+?) \((?P<fec>[0-9]+)\):? (?:"|\'\')(?P<tit>.+?)(?:"|\'\')')
volR = re.compile(ur' vol\. ([-0-9]+)[,.]')
numR = re.compile(ur' no\. ([-0-9]+)[,.]')
ppR = re.... | races1986/SafeLanguage | CEM/crearRef.py | Python | epl-1.0 | 3,470 | [
"ORCA"
] | fb7819d01ce8a9dfdec5f3a3021d8fa7cd1edd5099e1dd598c68a9af138ea335 |
# context.py - changeset and file context objects for mercurial
#
# Copyright 2006, 2007 Olivia Mackall <olivia@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from __future__ import absolute_import
import errno
impo... | smmribeiro/intellij-community | plugins/hg4idea/testData/bin/mercurial/context.py | Python | apache-2.0 | 102,025 | [
"VisIt"
] | 9c77d53cf1dd4669e821b650c0879d1322057816b6e18bd11e1238ffd602dca3 |
# Autodetecting setup.py script for building the Python extensions
#
import sys, os, importlib.machinery, re, optparse
from glob import glob
import importlib._bootstrap
import importlib.util
import sysconfig
from distutils import log
from distutils import text_file
from distutils.errors import *
from distutils.core i... | amyvmiwei/kbengine | kbe/src/lib/python/setup.py | Python | lgpl-3.0 | 97,472 | [
"VisIt"
] | 19054475a41e2bd28c219cc3f8b553e4d9db70cfa14cc4c84bc70f9035665579 |
from ase import Atom, Atoms
from ase.calculators.test import numeric_force
from gpaw import GPAW, Mixer
from gpaw.test import equal
a = 4.0
n = 16
atoms = Atoms([Atom('H', [1.234, 2.345, 3.456])],
cell=(a, a, a), pbc=True)
calc = GPAW(nbands=1,
gpts=(n, n, n),
txt=None,
... | qsnake/gpaw | gpaw/test/H_force.py | Python | gpl-3.0 | 883 | [
"ASE",
"GPAW"
] | f3de906dcbb09749cf0d267db942f88f79d880dca3a37f7bb59b7b3e8f3e9c1a |
"""
Data providers for genome visualizations.
"""
import os, sys, re
import pkg_resources
import itertools
import random
import math
pkg_resources.require( "numpy" )
pkg_resources.require( "bx-python" )
pkg_resources.require( "pysam" )
from bx.interval_index_file import Indexes
from bx.bbi.bigwig_file import BigWigFi... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/visualization/data_providers/genome.py | Python | gpl-3.0 | 63,991 | [
"Galaxy",
"pysam"
] | 3fc27af7fee8ca2201bd7a35b6c478c27ab2970e7d642bd9be32d49a273cbe22 |
#
#
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may n... | gouravshenoy/airavata | sandbox/simstream/example/openmm_example/openmm_log_consumer.py | Python | apache-2.0 | 1,822 | [
"OpenMM"
] | 047cc6cca69f8697caf0274d8e32ab156c788268761ced234ca32e8874fbb898 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
""" This unit test verifies that satellite server synchronization works
It is currently designed to be run from the commcare-hq install dir, like:
<install-dir>/python tests/deployment/testSync.py
TODO - clean this up so that we delete all submissions after each test
"""... | commtrack/temp-aquatest | tests/deployment/testSync.py | Python | bsd-3-clause | 26,984 | [
"Brian"
] | ff0f6a83cb139bd419e5850f13480ee323b955006e848dfc70fc24162bf1946d |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/sequence/_dna.py | Python | bsd-3-clause | 12,313 | [
"scikit-bio"
] | 341ed6fac9ad6c7416e2d98bc5f4cdb3335f2903b2249a5546eae5c9954ba1bc |
import psi4
import numpy as np
from psi4.driver.p4util.solvers import davidson_solver
from psi4.driver.procrouting.response.scf_products import SCFProducts
mol = psi4.geometry("""
O
H 1 1.1
H 1 1.1 2 104
symmetry c1
""")
psi4.set_options({"SAVE_JK": True})
psi4.set_options({"e_convergence": 1.e-1, "d_convergence": 1... | jgonthier/psi4 | tests/python/tddft/stab.py | Python | lgpl-3.0 | 1,400 | [
"Psi4"
] | 5425f5e80f7cd70064033be27f014e5717ccade60e241041f94dc5fc66d97203 |
from __future__ import division
from ase import Atoms, Atom
from multiasecalc.lammps import Bonds
import numpy as np
from numpy import pi, cos, sin, sqrt, dot
import random
random.seed(None)
np.random.seed(None)
from itertools import combinations, product
def distance_geometry(mol, bond_matrix, unit_indices, characte... | csmm/multiase | scripts/dgbuild.py | Python | gpl-2.0 | 7,325 | [
"ASE",
"LAMMPS"
] | 2ba87ee661c73c715271761ebc87bab746160bb6665a7a4e16aa864a3c365e56 |
""" NOTA BENE: This agent should NOT be run alone. Instead, it serves as a base class for extensions.
The TaskManagerAgentBase is the base class to submit tasks to external systems,
monitor and update the tasks and file status in the transformation DB.
This agent is extended in WorkflowTaskAgent and Reque... | coberger/DIRAC | TransformationSystem/Agent/TaskManagerAgentBase.py | Python | gpl-3.0 | 25,548 | [
"DIRAC"
] | 4b58b1fc956b55517c9887830496f170e7aa7231a476612dc936b1077d457586 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkVertexGlyphFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkVertexGlyphFilter.py | Python | bsd-3-clause | 495 | [
"VTK"
] | d81ac90d4a18e457cb91f270a0cbf4c026dba1b56ccce4693f97db5d82080428 |
import os
import markdown
import collections
import logging
log = logging.getLogger(__name__)
from MooseObjectSyntax import MooseObjectSyntax
from MooseParameters import MooseParameters
from MooseDescription import MooseDescription
from MooseActionSyntax import MooseActionSyntax
from MooseTextFile import MooseTextFile... | paulthulstrup/moose | python/MooseDocs/extensions/MooseMarkdown.py | Python | lgpl-2.1 | 6,758 | [
"MOOSE"
] | 7b3f97a257fc3e15055ae4b57f50f37594750a7f6a205899380ca0f729b6486c |
import glob
import os
from copy import copy
from datetime import datetime
import netCDF4 as nc
import numpy as np
import pandas as pd
from spatialnc.proj import add_proj
C_TO_K = 273.16
FREEZE = C_TO_K
# Kelvin to Celsius
K_TO_C = lambda x: x - FREEZE
def open_files_nc(myawsm):
"""
Open the netCDF files for... | USDA-ARS-NWRC/AWSF | awsm/interface/pysnobal_io.py | Python | gpl-3.0 | 12,601 | [
"NetCDF"
] | 6e5e9c956a17bb2a1fbb37973069037fc637f31cda183cf6ba26a39c5629512a |
#!/usr/bin/env python
'''
Parse logged data from accelerometer to compute translations in x, y, z and rotations
about these axes. Output as X3D text so that the data can be visualized in an X3D Browser.
--
Mike McCann
5 May 2011
$Id: accel2x3d.py 13595 2016-06-16 16:31:02Z mccann $
'''
import csv
from numpy import ... | stoqs/stoqs | stoqs/loaders/CCE/bed2netcdf/accel2x3d.py | Python | gpl-3.0 | 8,947 | [
"Brian"
] | 364fe7111c1fd300276cd4bc71c25dcdf2151e9231ddb612ffa022fc4046f629 |
# Export functions for NeuroML NetworkML 1.8.1
# TODO Should have been implemented in the client side in javascript
# given that the amount of data to transfer would have been smaller,
# and no computations would bog down the server.
# TODO Synapses are potentially incorrect: the properties of release
# are expected t... | catsop/CATMAID | django/applications/catmaid/control/export_NeuroML_Level3.py | Python | gpl-3.0 | 13,858 | [
"NEURON"
] | b575542c70b52a80e83f58804168c3b0d90a2fe417ebf85f0fbb0991d915849b |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RGseabase(RPackage):
"""Gene set enrichment data structures and methods.
This pack... | rspavel/spack | var/spack/repos/builtin/packages/r-gseabase/package.py | Python | lgpl-2.1 | 1,301 | [
"Bioconductor"
] | bb693e77cd1bac31f5dc497d02c3169acd16621f332e81c7a5984d021764162a |
########################################################################
# Author : Andrei Tsaregorodtsev
########################################################################
"""
Utilities for managing DIRAC configuration:
getCEsFromCS
getUnusedGridCEs
getUnusedGridSEs
getSiteUpdates
getSEUpdates
"""
... | chaen/DIRAC | ConfigurationSystem/Client/Utilities.py | Python | gpl-3.0 | 22,844 | [
"DIRAC"
] | 2e7006c692c8f1683147f40a73a30a4e258cb2889bf006518552a5d5a3ac5d90 |
import os
INSTALLED_APPS = [
'django.contrib.staticfiles',
'django.contrib.auth',
'django.contrib.contenttypes',
'django.contrib.messages', 'django.contrib.sessions',
'django.contrib.admin',
'octopus',
'test_app',
'django.contrib.sites'
]
SECRET_KEY = '1'
DEBUG = True
STATIC_URL = '/... | brmc/django-octopus | tests/settings.py | Python | mit | 1,705 | [
"Octopus"
] | 1fa1dbe8aa5d0cc3747cb2d9058bda3a17c3f56b86b5cc58204e6a571fb06170 |
import test.support
# Skip tests if _multiprocessing wasn't built.
test.support.import_module('_multiprocessing')
# Skip tests if sem_open implementation is broken.
test.support.import_module('multiprocessing.synchronize')
# import threading after _multiprocessing to raise a more revelant error
# message: "No module n... | Microvellum/Fluid-Designer | win64-vc/2.78/python/lib/test/test_concurrent_futures.py | Python | gpl-3.0 | 25,887 | [
"Brian"
] | 8388035d2591824a63cef988714ec98d608c6bb4a05ab13f92c94b2ecb4b16f0 |
import theano.tensor as T
import theano.tensor.nnet as Tnn
import numpy as np
import theano
import nonlinearity
class GaussianHidden(object):
"""
Stochastic layer: Gaussian distribution, linear transpose + random sampling z
"""
def __init__(self, rng, input, n_in, n_out, W_var=None, b_var=None, W_me... | zhenxuan00/mmdgm | conv-mmdgm/layer/GaussianHidden.py | Python | mit | 3,834 | [
"Gaussian"
] | 2c716742620de5c2384e18a7197c7b161ce598771aab62e161fddc895263b556 |
#!/usr/bin/python
BoysNames = [ "Aaron", "Adam", "Alexander", "Andrew", "Anthony", "Austin",
"Benjamin", "Blake", "Brandon", "Brendan", "Brian", "Brady",
"Bryson", "Charles", "Christian", "Christopher", "Cody", "Conner",
"Daniel", "Dean", "Derek", "Donald", "Dylan", "Edward", ... | linuxsoftware/dominoes | davezdominoes/gamecoordinator/utils/name.py | Python | agpl-3.0 | 26,257 | [
"Amber",
"Brian",
"CRYSTAL",
"Dalton",
"FLEUR",
"TINKER"
] | 4628a380229a58ebb9c0eb0465af8e3abacd5a4a0beb8fe7b9d743233423409c |
#---------------------------------------#
# This file is part of EbmLib.
#
# EbmLib is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
#... | thomlake/EbmLib | ebmlib/srrbm/cdktrainer.py | Python | gpl-3.0 | 6,491 | [
"CDK"
] | 6a1c3270ec1e0e1d5e11ce05174652cd948f19c09610057bdc35a42c3f889c48 |
#----------------------------------------------------------
#Example to run a multi-dimensional GP analysis with pyaneti
#Barragan O., 2021
#This analysis reproduces the full analysis of K2-100 presented in
#http://dx.doi.org/10.1093/mnras/stz2569
#----------------------------------------------------------
#----------... | oscaribv/pyaneti | inpy/example_full_k2100/input_fit.py | Python | gpl-3.0 | 7,885 | [
"Gaussian"
] | c7d2f9a6bec3a5f5a72a67c9acb9e7fd4241d8d4d3f84b2b9af3f8832eee3a5e |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | jturney/psi4 | psi4/driver/p4util/optproc.py | Python | lgpl-3.0 | 5,468 | [
"Psi4"
] | 3404b2eadf8147c9a25a5035f0cd41dc87a08433113b2868a1e2ad9634681fb2 |
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software... | mardom/GalSim | galsim/config/gsobject.py | Python | gpl-3.0 | 22,000 | [
"Galaxy"
] | c4825923d029ce98e4d84d1a7ddcbaa5bf2b419128ca5bec848503d392cfab70 |
#!/usr/bin/python
"""
Copyright 2013 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of th... | clreinki/GalaxyHarvester | ghShared.py | Python | agpl-3.0 | 2,405 | [
"Galaxy"
] | 83f42b219df2e26ddd24905ff24e6f9ed5dafea9f80c7c902ce18749241d7756 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
An implementation of a red–black tree as it is described in
Cormen, Leiserson, Rivest, Stein 2nd edition pg 273.
A the height of a red-black tree is never bigger than
2*log_2(n+1). This is achived with these properties:
RB1) Every node is either r... | saisai/algorithms_by_other | datastructures/redBlackTree.py | Python | mit | 20,193 | [
"VisIt"
] | cd6ec130751714c3d4424cbb7c5fc5aeb0f5d4aa841894ccf869f87b6aad627b |
# -*- coding: utf-8 -*-
# Copyright (c) 2015, Alex Grigorevskiy
# Licensed under the BSD 3-clause license (see LICENSE.txt)
"""
Test module for state_space_main.py
"""
import unittest
import numpy as np
import matplotlib.pyplot as plt
from scipy.stats import norm
import GPy.models.state_space_setup as ss_setup
import... | mikecroucher/GPy | GPy/testing/state_space_main_tests.py | Python | bsd-3-clause | 44,812 | [
"Gaussian"
] | f322c0281580d389193bfa1e57ae6cc7878ee943f749f66afdd609671a600148 |
from PyQt4 import QtCore, QtGui
import overlayDialogBase
import ilastik.gui.overlaySelectionDlg
from ilastik.core.overlays.thresholdOverlay import ThresholdOverlay
#*******************************************************************************
# S l i d e r R e c e i v e r ... | ilastik/ilastik-0.5 | ilastik/gui/overlayDialogs/multivariateThresholdDialog.py | Python | bsd-2-clause | 8,038 | [
"Gaussian"
] | 0580773e57be5194d6ed065b4314aac2c02c2785eec4b8255dd15d7148da4424 |
import sys
import urllib
import urlparse
from resources import wwe
import xbmcaddon
import xbmcgui
import xbmcplugin
from datetime import datetime, timedelta
import pickle
base_url = sys.argv[0]
addon = xbmcaddon.Addon()
addon_handle = int(sys.argv[1])
args = urlparse.parse_qs(sys.argv[2][1:])
media_path = addon.getAd... | alegag/plugin.video.wwen | wwen_plugin.py | Python | gpl-3.0 | 11,323 | [
"VisIt"
] | 7610aa65756744a2ed99196dc666554d39025f5996f2784757d1c8947e0bece9 |
#!/usr/bin/python
# lightLEDs.py
# Button press loops through LEDs like this (0 is led off, 1 is led on): 000, 100, 110, 111, 011, 001, 000, 100, 110, 111, 011, 001, 000 etc.
# Author : Zachary Igielman
import RPi.GPIO as GPIO, time, sys
GPIO.setmode(GPIO.BOARD)
GPIO.setup(11, GPIO.OUT) #red
GPIO.setup(13, GPIO.OUT)... | soslug/projects | rpi/python_resources/smstext-and mypifi-code/lightLEDs.py | Python | gpl-3.0 | 852 | [
"Amber"
] | fc34d4fb3bc6f559e8a471b8e0e1a9769857dde3b4c2c2958669ad521ffbffdb |
#
# 1st version by Fulvio Paleari
# This file is part of yambopy
#
import os
import re
import numpy as np
from qepy import PwIn
from yambopy.lattice import *
from itertools import product
import copy
from math import *
import fractions as frc
# Dimensional constants for reference (actually only b2a is really used in th... | alexmoratalla/yambopy | qepy/supercell.py | Python | bsd-3-clause | 18,964 | [
"CRYSTAL",
"Quantum ESPRESSO"
] | 25c52321b83b4cff304905eafce104f058ac3eecab904bee403812694d34f682 |
#!/usr/bin/env python3
import argparse, sys, math
def read_cmd():
"""Reads command line params"""
desc = "Generate even-tempered basis set for TeraChem"
parser = argparse.ArgumentParser(description=desc)
parser.add_argument("-n", dest="nbasis", type=int, required=True, help="Number of basis funcs")
par... | PHOTOX/photoxrepo | INPUTS/FANOCI/BASIS-GENERATION/gen_even_tempered_basis.py | Python | mit | 1,729 | [
"Gaussian",
"TeraChem"
] | 597c238ffedd06a6dab77670eedbe382b1600ebf2499320a6f4c42a53a1c6303 |
from itertools import combinations_with_replacement
import numpy as np
from scipy import ndimage as ndi
from scipy import stats
from ..util import img_as_float, pad
from ..feature import peak_local_max
from ..feature.util import _prepare_grayscale_input_2D
from ..feature.corner_cy import _corner_fast
from ._hessian_d... | ofgulban/scikit-image | skimage/feature/corner.py | Python | bsd-3-clause | 26,732 | [
"Gaussian"
] | 26b9dfed7ea0b784046b4ab40a628ccd0207f44f60f9ec1dc89ae07c57e20e9e |
#!/usr/bin/env python
"""
Use the 1D data interpolation/extrapolation problem to benchmark convergence
variance. Comparison of training methods, EKF vs SGD.
"""
# Dependencies
from __future__ import division
import numpy as np; npl = np.linalg
import matplotlib.pyplot as plt
import matplotlib.mlab as mlab
import kalma... | jnez71/kalmaNN | demos/1d_fit_analysis.py | Python | mit | 1,764 | [
"NEURON"
] | 7d27c7aeae0ef9b04bb2985906ef9aa6d36119ce22c413bc25a3e0eb3fb5395d |
# -*- coding: utf-8 -*-
"""
Ideally, this script should
take (user?) inputs to determine x_predicted, y_predicte, and z_predicted arrays
take inputs from the second script to enter in data (that is, the temperature (T_time_avg_3d) and position (xyz_observed) data that was augmented in the second script).
TODO:
outpu... | isomerase/GP-temperature-interpolation | GaussianProc_predictor_3D.py | Python | mit | 3,256 | [
"Gaussian"
] | 00266f6ef9e9f611dcc7f66d12364cf76db6608dec35efc9a6a802db2e2e8948 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
# Copyright 2017 The Chromium OS Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Autosuspend udev rule generator
This script is executed at build time to generate udev rules. The
resu... | walyong/systemd | tools/chromiumos/gen_autosuspend_rules.py | Python | gpl-2.0 | 7,167 | [
"Octopus"
] | 6c5305b284bfc9ad035b070ecf782fc52c064e5690cbbf883abc40637e7d5649 |
# Version: 0.17
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, and pypy
* [![Latest Version]
(http... | CINPLA/exdir | versioneer.py | Python | mit | 68,821 | [
"Brian"
] | e194903e591c769a92f08ff86db25eb3bab9771b5b00738211590c1081adebdd |
#!/usr/local/bin/python
# encoding: utf-8
"""
*Import ned_d catalogue into sherlock-catalogues database*
:Author:
David Young
"""
from __future__ import print_function
from __future__ import division
from builtins import zip
from past.utils import old_div
import sys
import os
os.environ['TERM'] = 'vt100'
import re... | thespacedoctor/sherlock | sherlock/imports/ned_d.py | Python | mit | 24,917 | [
"Galaxy"
] | 074dc285ae69327823e699803efcfb8109a32b2013eebb325be98ed8bcd7b8f9 |
from __future__ import division
from __future__ import print_function
import matplotlib.pyplot as plt
import numpy as np
import sys
import os
import datetime
from netCDF4 import Dataset
import netCDF4
import time_tools_attractor as ti
import io_tools_attractor as io
import data_tools_attractor as dt
imp... | meteoswiss-mdr/precipattractor | pymodules/load_forecasts.py | Python | gpl-3.0 | 46,753 | [
"NetCDF"
] | a2acbbeaac11b0c199423288f13155a5f6da362d61783ab80ee9ace28bf6b747 |
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
repository_name = 'bed_to_gff_0130'
repository_description = "Converter: BED to GFF"
repository_long_description = "Convert bed to gff"
category_name = 'Test 0130 Datatype Converters'
category_description = 'Test 0130 Datatype Converters'
'''
1) I... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/tool_shed/functional/test_1130_datatype_converters.py | Python | gpl-3.0 | 5,777 | [
"Galaxy"
] | bdc0c9a4fbdac3852dde9db6160b1a6a71cd62a3cb35649cce09449d58fbfa7e |
"""
This pipeline is intended to extract Haralick features from T2W images.
"""
import os
import numpy as np
from protoclass.data_management import T2WModality
from protoclass.data_management import GTModality
from protoclass.preprocessing import RicianNormalization
from protoclass.preprocessing import GaussianNorm... | I2Cvb/mp-mri-prostate | pipeline/feature-extraction/t2w/pipeline_extraction_gabor_t2w.py | Python | mit | 4,610 | [
"Gaussian"
] | 1c3bda81cb1f0b688310e2f6aa9f1fb540a5dd89ead56dbd0848486b1ec93ddd |
#!/usr/bin/python
# =============================================================================================
# MODULE DOCSTRING
# =============================================================================================
"""
Test restraints module.
"""
# =====================================================... | choderalab/yank | Yank/tests/test_restraints.py | Python | mit | 28,233 | [
"NetCDF",
"OpenMM"
] | 69c8b5b5daf4b8bfd7feb39c013f646277fdbedf0f2cc8e937925b23311f5aac |
#!/usr/bin/env python
"""Ninja build configurator for mdns library"""
import sys
import os
sys.path.insert( 0, os.path.join( 'build', 'ninja' ) )
import generator
dependlibs = [ 'network', 'foundation' ]
generator = generator.Generator( project = 'mdns', dependlibs = dependlibs, variables = [ ( 'bundleidentifier'... | rampantpixels/mdns_lib | configure.py | Python | unlicense | 3,163 | [
"BLAST"
] | 654e87a2d709657fbde00e65c8b9de1791b83aad4ae0d86f3d83cfc3cf9cffb1 |
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